Software to work with 3D scan and prototyping
As this is a blender specific website, may I recommend blender?
Blender has some basic tools for preparing models for printing, see this, and there are plenty of tutorials out there, but here's a few things to note that most of them don't cover:


Blender unit system is not like CAD software. See here for info on working with it. I would recommend using metric, as imperial can get quite messy.  If you need models in inches, change the scale factor (multiply by 25.4, as that's the number of mm per inch) when exporting.
Blender is very flexible with normals (the direction a face points).  3d printing software is not.  Before exporting go into edit mode and hit ctrl+N to recalculate the normals.
Use the decimate modifier to simplify geometry before exporting. Enabling planar mode on this modifier is one way to make edges smoother.
The laplacian smooth modifier may also be helpful if the data is noisy.
The shrinkWrap modifier may be good, if the data isn't too complex.
A good approach to learning to do this with blender would be  
Import the file to blender as a mesh object.
Apply a decimate or smooth modifier to the model, maybe play around with some of the others too, until you find what gets good results.
Apply the modifiers, after making a backup of the scene or file.
Do any manual editing of the mesh needed
Export as an stl file with an appropriate scale factor.